Cylotrimethylenetrinitramine (RDX), with the chemical formula C3H6N6O6,is an energetic organic molecule used widely in military and industrial commodities ofexplosives. By stimulating RDX through exerting temperature or mechanical conditionssuch as impact or friction, decomposition reaction occurs at a very high rate. Moleculardynamics techniques and LAMMPS code with Rea...

Abstract Disordered packings of non-spherical particles and their mixtures are abundant in nature, but have so far attracted only few systematic studies. Previous investigations binary specific convex shapes established two generic properties: (i) the existence a unique density maximum when shape or mixture composition species varied; (ii) validity an ideal mixing law indicating that packing is...

The most widely used technique to allow for parallel simulations in molecular dynamics is spatial domain decomposition, where the physical geometry divided into boxes, one per processor. This can inherently produce computational load imbalance when either distribution of particles or cost particle not uniform. paper shows benefits using a hybrid MPI+OpenMP model deal with this imbalance. We con...

From the images of HR-TEM, FE-SEM, and AFM, the cold welding of gold nanoparticles (AuNPs) on a mica substrate is observed. The cold-welded gold nanoparticles of 25 nm diameters are found on the mica substrate in AFM measurement whereas the size of cold welding is limited to 10 nm for nanowires and 2~3 nm for nanofilms. Contrary to the nanowires requiring pressure, the AuNPs are able to rotate ...

Generalized Langevin dynamics (GLD) arise in the modeling of a number of systems, ranging from structured fluids that exhibit a viscoelastic mechanical response, to biological systems, and other media that exhibit anomalous diffusive phenomena. Molecular dynamics (MD) simulations that include GLD in conjunction with external and/or pairwise forces require the development of numerical integrator...

The current state of practice in supercomputer resource allocation places jobs from different users on disjoint nodes both in terms of time and space. While this approach largely guarantees that jobs from different users do not degrade one another’s performance, it does so at high cost to system throughput and energy efficiency. This focused study presents job striping, a technique that signifi...

Molecular Dynamics (MD) simulations are often used for comprehending evolving deformation mechanisms in materials at the atomic scale and also for assessing continuum-scale material properties. A major limitation of conventional MD simulations is that very small MD time-scale ( fs), restrict the achievable strain-rates to be much higher ( 10 or higher) than experimentally observed rates, needed...

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally ...

The use of accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid highperformance computers, machines with more than one type of floating-point processor, are now becoming more prevalent due to these advantages...

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this paper, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for multi-core architectures. As hybrid parallelism allows better levera...